Methods of fabricating an addressable array of biopolymer probes

ABSTRACT

A method of fabricating an addressable array of biopolymer probes on a substrate according to a target array pattern using a deposition apparatus, and a deposition apparatus which can execute the method and computer program products for the apparatus. The deposition apparatus which, when operated according to a target drive pattern based on nominal operating parameters of the apparatus, provides the probes on the substrate in the target array pattern. The method includes examining at least one operating parameter for an error from a nominal value which error will result in use of the target drive pattern producing a discrepancy between the target array pattern and an actual array pattern deposited. When an error is detected deriving, based on the error, a corrected drive pattern different from the target drive pattern such that use of the corrected drive pattern results in a reduced discrepancy between the target and actual array patterns.

FIELD OF THE INVENTION

[0001] This invention relates to arrays, particularly polynucleotidearrays such as DNA arrays, which are useful in diagnostic, screening,gene expression analysis, and other applications.

BACKGROUND OF THE INVENTION

[0002] Polynucleotide arrays (such as DNA or RNA arrays), are known andare used, for example, as diagnostic or screening tools. Such arraysinclude regions (sometimes referenced as features) of usually differentsequence polynucleotides arranged in a predetermined configuration on asubstrate. The arrays, when exposed to a sample, will exhibit anobserved binding pattern. This binding pattern can be detected, forexample, by labeling all polynucleotide targets (for example, DNA) inthe sample with a suitable label (such as a fluorescent compound), andaccurately observing the fluorescence pattern on the array. Assumingthat the different sequence polynucleotides were correctly deposited inaccordance with the predetermined configuration, then the observedbinding pattern will be indicative of the presence and/or concentrationof one or more polynucleotide components of the sample.

[0003] Biopolymer arrays can be fabricated using either in situsynthesis methods or deposition of the previously obtained biopolymers.The in situ synthesis methods include those described in U.S. Pat. No.5,449,754 for synthesizing peptide arrays, as well as WO 98/41531 andthe references cited therein for synthesizing polynucleotides(specifically, DNA). Such in situ synthesis methods can be basicallyregarded as iterating the sequence of depositing droplets of: (a) aprotected monomer onto predetermined locations on a substrate to linkwith either a suitably activated substrate surface (or with a previouslydeposited deprotected monomer); (b) deprotecting the deposited monomerso that it can now react with a subsequently deposited protectedmonomer; and (c) depositing another protected monomer for linking.Different monomers may be deposited at different regions on thesubstrate during any one iteration so that the different regions of thecompleted array will have different desired biopolymer sequences. One ormore intermediate further steps may be required in each iteration, suchas oxidation and washing steps. The deposition methods basically involvedepositing biopolymers at predetermined locations on a substrate whichare suitably activated such that the biopolymers can link thereto.Biopolymers of different sequence may be deposited at different regionsof the substrate to yield the completed array. Washing or otheradditional steps may also be used.

[0004] Typical procedures known in the art for deposition ofpolynucleotides, particularly DNA such as whole oligomers or cDNA, areto load a small volume of DNA in solution in one or more drop dispenserssuch as the tip of a pin or in an open capillary and, touch the pin orcapillary to the surface of the substrate. Such a procedure is describedin U.S. Pat. No. 5,807,522. When the fluid touches the surface, some ofthe fluid is transferred. The pin or capillary must be washed prior topicking up the next type of DNA for spotting onto the array. Thisprocess is repeated for many different sequences and, eventually, thedesired array is formed. Alternatively, the DNA can be loaded into adrop dispenser in the form of an inkjet head and fired onto thesubstrate. Such a technique has been described, for example, in PCTpublications WO 95/25116 and WO 98/41531, and elsewhere. This method hasthe advantage of non-contact deposition. Still other methods includepipetting and positive displacement pumps such as the Biodot equipment(available from Bio-Dot Inc., Irvine Calif., USA).

[0005] In array fabrication, the quantities of DNA available for thearray are usually very small and expensive. Sample quantities availablefor testing are usually also very small and it is therefore desirable tosimultaneously test the same sample against a large number of differentprobes on an array. These conditions require use of arrays with largenumbers of very small, closely spaced features. It is important in sucharrays that features actually be present, that they are put downaccurately in the desired pattern, are of the correct size, and that theDNA is uniformly coated within the feature. Normally, in an automatedapparatus the features are deposited according to a target arraypattern. A target drive pattern is created from the target arraypattern, which target drive pattern contains the instructions fordriving the various components so as to provide the probes on thesubstrate in the target array pattern. The target drive pattern iscreated on the assumption that all components of the depositionapparatus are in their expected or normal (“nominal”) positions andoperating according to nominal parameters.

[0006] However, the present invention realizes that every component inan array deposition apparatus is subject to variances in its parameterswithin, or sometimes even outside of, normal tolerances for suchcomponent. For example, a dispensing head used to dispense fluiddroplets to form the array, may have jets which vary slightly in thesize of the droplets dispensed, the orientation of the jets with respectto one another, or the orientation of the head itself in the apparatusmay be slightly off from a nominal position. While such variances can bereduced by constructing a dispensing apparatus with components of highertolerance (that is, less variation), this can increase cost.Furthermore, the present invention realizes that while a given set ofparameters may exist during manufacture of a given batch of arrays,these parameters may change over time. For example, thermal expansion orof components or slight displacement of them from their originalpositions over long periods of operation, leads to variance in positionparameters. These effects result in use of the target drive pattern notproducing the target array on the substrate. That is, there is adiscrepancy between the target array pattern and the actual arraypattern deposited. Such discrepancy may include mislocation of features,or features not being of the correct size. These discrepancies can occurin each cycle of the in situ process, or during deposition ofpresynthesized polynucleotides.

[0007] It would be useful then, to provide a means by which arrays canbe fabricated with an actual array pattern which is close to the targetarray pattern. It would also be useful if such means was relativelyreliable and not overly costly.

SUMMARY OF THE INVENTION

[0008] The present invention then, provides in one aspect, a method offabricating an addressable array of biopolymer probes on a substrateaccording to a target array pattern, using a deposition apparatus. Thedeposition apparatus, when operated according to a target drive patternbased on nominal operating parameters of the apparatus, provides theprobes on the substrate in the target array pattern. The method includesexamining at least one operating parameter of the apparatus for an errorfrom a nominal value which error will result in use of the target drivepattern producing a discrepancy between the target array pattern and anactual array pattern deposited. When an error is detected, a correcteddrive pattern different from the target drive pattern is derived, basedon the error, such that use of the corrected drive pattern results in areduced discrepancy between the target and actual array patterns.

[0009] The method may also include operating the deposition apparatusaccording to the corrected drive pattern. Furthermore, the presentinvention can be used to deposit different types of biopolymers or evenother different chemical moieties, including peptides andpolynucleotides such as DNA or RNA. Thus, various additional embodimentsof the invention can be described by replacing biopolymer probes in thedescriptions herein, with moieties. The target drive pattern caninitially be saved in a memory of the deposition apparatus, and thecorrected drive pattern can also optionally be saved in the memory (forexample, either after or during its derivation). In one particularconstruction, the deposition apparatus includes a dispensing head todispense fluid droplets containing the probes or probe precursors (forexample, monomers), and a transport system to move at least one of thedispensing head and substrate relative to the other as the droplets aredispensed from the head, so as to form the array. In this case, thedrive pattern controls operation of the transport system. The saving ofthe corrected drive pattern may, for example, be done prior to operatingthe dispensing apparatus. As an alternative, the corrected drive patternmay be derived by modifying, based on the detected error, instructionsto at least one deposition apparatus component based on the target drivepattern during deposition of the probes to form the array. For example,an instruction based on the target drive pattern may be sent to theforegoing dispensing head but that instruction is modified, beforeactually driving the head in some manner, based on the detected error.In this arrangement then, the corrected drive pattern is derived duringapparatus operation.

[0010] The at least one operating parameter can be selected from one ormore of any parameter which would affect the actual array patterndeposited. For example, these may include: a position of the dispensinghead or any other dispensing apparatus component; the accuracy of anencoder used to detect the position of the dispensing head or thesubstrate; the accuracy in an ability of the transport system to movethe substrate or head to an expected location in response to a command(for example, deviation of actual movement from a corresponding nominalaxis of movement); or the position of a position of a nozzle in amultiple nozzle dispensing head. Note that “position” includes linearposition as well as orientation of one component with respect to theother, and may be an absolute or relative quantity (for example, theposition of a dispensing jet in the head relative to another jet in thathead, or relative to the substrate). Parameters can be directly examined(such as by examining movement of the transport system or nozzle), orindirectly examined (such as by examining the actual results fromprevious depositions of the apparatus and comparing with expectedresults). Such examination can be made during formation of a givenarray, or obtained during (or from) previous depositions from theapparatus, for example either test depositions (sometimes referenced as“test prints”) or a previous array deposition (such as an immediatelypreceding array deposition).

[0011] Another aspect of the method of the present invention, the targetdrive pattern is stored in a memory of the deposition apparatus, andwhen an error from a nominal value exists in at least one operatingparameter, a corrected drive pattern is derived from the target drivepattern such that use of the corrected drive pattern results in areduced discrepancy between the target and actual array patterns.

[0012] The present invention also provides an apparatus which, in one ormore aspects, may be of a type described in connection with any of theabove methods. Such an apparatus includes, in one aspect, a sensor whichsenses at least one operating parameter for an error from a nominalvalue which error will result in use of the target drive patternproducing a discrepancy between the target array pattern and an actualarray pattern deposited. This apparatus also includes a processor which,when an error is detected by the sensor derives, based on the error, acorrected drive pattern different from the target drive pattern suchthat use of the corrected drive pattern results in a reduced discrepancybetween the target and actual array patterns.

[0013] The apparatus may also include a memory accessible by theprocessor to save the target drive pattern, and wherein the processor,when no error is detected, causes the apparatus to operate in accordancewith the target drive pattern. The processor may further optionally savea corrected drive pattern in the memory. Alternatively, the processormay derive the corrected drive pattern during deposition of the probesto form the array, by modifying, based on the detected error,instructions to at least one apparatus component based on the targetdrive pattern, as mentioned above. The apparatus may further include adispensing head and a transport system controlled by the processor, asalready described. Various parameters are also described above.

[0014] In another aspect, the apparatus includes a memory to store atarget drive pattern based on nominal operating parameters of theapparatus to provide the probes on the substrate in the target arraypattern. This aspect of the apparatus also includes a processor toreceive an error indication of the type already described, and to derivethe corrected drive pattern.

[0015] The present invention further provides a computer program productwhich can be used on one or more of the apparatus types alreadydescribed. This computer program product includes a computer readablestorage medium having a computer program stored on it which, when loadedinto a computer, instructs the processor to execute the steps describedabove.

[0016] The present invention then, including methods, apparatus, andcomputer program products thereof, can provide any one or more, of anumber of useful benefits. For example, arrays can be fabricated with anactual array pattern which is close to the target array pattern.Further, the invention is relatively reliable and not overly costly.

BRIEF DESCRIPTION OF THE DRAWINGS

[0017]FIG. 1 is a perspective view of a substrate bearing multiplearrays, as may be produced by a method and apparatus of the presentinvention;

[0018]FIG. 2 is an enlarged view of a portion of FIG. 1 showing some ofthe identifiable individual regions (or “features”) of a single array ofFIG. 1;

[0019]FIG. 3 is an enlarged cross-section of a portion of FIG. 2;

[0020]FIG. 4 is a schematic view of apparatus of the present invention;

[0021]FIG. 5 is a flowchart illustrating a method of the presentinvention; and

[0022]FIGS. 6 through 8 are memory images illustrating the operation ofthe present invention.

[0023] To facilitate understanding, identical reference numerals havebeen used, where practical, to designate identical elements that arecommon to the figures.

DETAILED DESCRIPTION OF EMBODIMENTS OF THE INVENTION

[0024] In the present application, unless a contrary intention appears,the following terms refer to the indicated characteristics. A“biopolymer” is a polymer of one or more types of repeating units.Biopolymers are found in biological systems and particularly includepeptides or polynucleotides, as well as such compounds composed of orcontaining amino acid or nucleotide analogs or non-nucleotide groups.This includes polynucleotides in which the conventional backbone hasbeen replaced with a non-naturally occurring or synthetic backbone, andnucleic acids in which one or more of the conventional bases has beenreplaced with a synthetic base capable of participating in Watson-Cricktype hydrogen bonding interactions. Polynucleotides include single ormultiple stranded configurations, where one or more of the strands mayor may not be completely aligned with another. A “nucleotide” refers toa subunit of a nucleic acid and has a phosphate group, a 5 carbon sugarand a nitrogen containing base, as well as analogs of such subunits.Specifically, a “biopolymer” includes DNA (including cDNA), RNA andoligonucleotides. An “oligonucleotide” generally refers to a nucleotidemultimer of about 10 to 100 nucleotides in length, while a“polynucleotide” includes a nucleotide multimer having any number ofnucleotides. A “biomonomer” references a single unit, which can belinked with the same or other biomonomers to form a biopolymer (forexample, a single amino acid or nucleotide with two linking groups oneor both of which may have removable protecting groups). A biomonomerfluid or biopolymer fluid reference a liquid containing either abiomonomer or biopolymer, respectively (typically in solution). An“addressable array” includes any one or two dimensional arrangement ofdiscrete regions (or “features”) bearing particular biopolymer moieties(for example, different polynucleotide sequences) associated with thatregion and positioned at a particular location on the substrate (an“address”). These regions may or may not be separated by interveningspaces. It will also be appreciated that throughout the presentapplication, words such as “upper”, “lower” and the like are used withreference to a particular orientation of the apparatus with respect togravity, but it will be understood that other operating orientations ofthe apparatus or any of its components, with respect to gravity, arepossible. Reference to a “droplet” being dispensed from a pulse jetherein, merely refers to a discrete small quantity of fluid (usuallyless than about 1000 pL) being dispensed upon a single pulse of thepulse jet (corresponding to a single activation of an ejector) and doesnot require any particular shape of this discrete quantity. However, itwill be understood that a given feature may be formed from one ormultiple pulses from one or multiple nozzles. When a “spot” is referredto, this may reference a dried spot on the substrate resulting fromdrying of one or more dispensed droplets, or a wet spot on the substrateresulting from one or more dispensed droplets which have not yet dried,depending upon the context. The dried spot will normally be theresulting feature in the case of deposition of pre-synthesizedbiopolymer, but will not be the resulting feature in the case of in situformation synthesis of biopolymers. Reference to “viewing” indicatesobservation by any optical device, such as a camera. The head orsubstrate moving “as” droplets are dispensed includes actual movementduring and/or between the dispensing of multiple droplets. “Fluid” isused herein to reference a liquid. By one item being “remote” fromanother is referenced that they are at least in different buildings, andmay be at least one, at least ten, or at least one hundred miles apart.

[0025] Referring first to FIGS. 1-3, typically the present inventionwill produce multiple identical arrays 12 (only some of which are shownin FIG. 1) across the complete upper surface 11a of a single substrate10. However, the arrays 12 produced on a given substrate need not beidentical and some or all could be different. Each array 12 will containmultiple spots or features 16. A typical array 12 may contain from 100to 100,000 features. All of the features 16 may be different, or some orall could be the same. Each feature carries a predeterminedpolynucleotide having a particular sequence, or a predetermined mixtureof polynucleotides. This is illustrated schematically in FIG. 3 wheredifferent regions 16 are shown as carrying different polynucleotidesequences. Substrate 10 also includes fiducial markings 18 on uppersurface 11 a, for purposes which will be described below. Fiducialmarkings 18 can be scratches, ink marks, metallized markings (forexample, chromium) markers, laser ablated grooves, or any other suitablemarking.

[0026] Referring to FIG. 4 the apparatus shown includes a substratestation 20 on which can be mounted a substrate 10. Pins or similar means(not shown) can be provided on substrate station 20 by which toapproximately align substrate 10 to a nominal position thereon.Substrate station 20 can include a vacuum chuck connected to a suitablevacuum source (not shown) to retain a substrate 10 without exerting toomuch pressure thereon, since substrate 10 is often made of glass.

[0027] A dispensing head 210 is retained by a head retainer 208. Head210 has fiducial markings 211, for purposes described below, and can bepositioned at any position facing substrate 10 by means of a positioningsystem. The positioning system includes a carriage 62 connected to afirst transporter 60 controlled by processor 140 through line 66, and asecond transporter 100 controlled by processor 140 through line 106.Transporter 60 and carriage 62 are used execute one axis positioning ofstation 20 (and hence mounted substrate 10) facing the dispensing head210, by moving it in the direction of nominal axis 63, while transporter100 is used to provide adjustment of the position of head retainer 208(and hence head 210) in a direction of nominal axis 204. In this manner,head 210 can be scanned line by line, by scanning along a line oversubstrate 10 in the direction of axis 204 using transporter 100, whileline by line movement of substrate 10 in a direction of axis 63 isprovided by transporter 60. Head 210 may also optionally be moved in avertical direction 202, by another suitable transporter (not shown).However, it will be appreciated that other scanning configurations couldbe used. However, it will be appreciated that both transporters 60 and100, or either one of them, with suitable construction, could be used toperform the foregoing scanning of head 210 with respect to substrate 10.Thus, when the present application refers to “positioning” one element(such as head 210) in relation to another element (such as one of thestations 20 or substrate 10) it will be understood that any requiredmoving can be accomplished by moving either element or a combination ofboth of them. An encoder 30 communicates with processor 140 to providedata on the exact location of substrate station 20 (and hence substrate10 if positioned correctly on substrate station 20), while encoder 34provides data on the exact location of holder 208 (and hence head 210 ifpositioned correctly on holder 208). Any suitable encoder, such as anoptical encoder, may be used which provides data on linear position.Angular positioning of substrate station 20 is provided by a transporter120, which can rotate substrate station 20 about axis 202 under controlof processor 140. Typically, substrate station 20 (and hence a mountedsubstrate) is rotated by transporter 120 under control of processor 140in response to an observed angular position of substrate 10 asdetermined by processor 140 through viewing one or more fiducial markson substrate 10 (particularly fiducial marks 18) with camera 304. Thisrotation will continue until substrate 10 has reached a predeterminedangular relationship with respect to dispensing head 210. In the case ofa square or rectangular substrate, the mounted substrate 10 willtypically be rotated to align one edge (length or width) with the scandirection of head 210 along axis 204.

[0028] Head 210 may be of a type commonly used in an ink jet type ofprinter and may, for example, have one hundred fifty drop dispensingorifices in each of two parallel rows, six chambers for holdingpolynucleotide solution communicating with the three hundred orifices,and three hundred ejectors which are positioned in the chambers oppositea corresponding orifice. Each ejector is in the form of an electricalresistor operating as a heating element under control of processor 140(although piezoelectric elements could be used instead). Each orificewith its associated ejector and portion of the chamber, defines acorresponding pulse jet with the orifice acting as a nozzle. Thus, thereare three hundred pulse jets in this configuration, although it will beappreciated that head 210 could, for example, have more or less pulsejets as desired (for example, at least ten or at least one hundred pulsejets). In this manner, application of a single electric pulse to anejector causes a droplet to be dispensed from a corresponding orifice.In the foregoing configuration, typically about twenty orifices in eachgroup of six reservoirs (many of the orifices are unused and are pluggedwith glue), will be dispensing the same fluid. Certain elements of thehead 210 can be adapted from parts of a commercially available thermalinkjet print head device available from Hewlett-Packard Co. as part no.HP51645A. The foregoing head 210 and other suitable dispensing headdesigns are described in more detail in U.S. patent application entitled“A MULTIPLE RESERVOIR INK JET DEVICE FOR THE FABRICATION OF BIOMOLECULARARRAYS” Ser. No. 09/150,507 filed Sep. 9, 1998. However, other headconfigurations can be used, for example a head with thirty reservoirs,and even multiple heads can also be used as desired.

[0029] As is well known in the ink jet print art, the amount of fluidthat is expelled in a single activation event of a pulse jet, can becontrolled by changing one or more of a number of parameters, includingthe orifice diameter, the orifice length (thickness of the orificemember at the orifice), the size of the deposition chamber, and the sizeof the heating element, among others. The amount of fluid that isexpelled during a single activation event is generally in the rangeabout 0.1 to 1000 pL, usually about 0.5 to 500 pL and more usually about1.0 to 250 pL. A typical velocity at which the fluid is expelled fromthe chamber is more than about 1 m/s, usually more than about 10 m/s,and may be as great as about 20 m/s or greater. As will be appreciated,if the orifice is in motion with respect to the receiving surface at thetime an ejector is activated, the actual site of deposition of thematerial will not be the location that is at the moment of activation ina line-of-sight relation to the orifice, but will be a location that ispredictable for the given distances and velocities.

[0030] The sizes of the features can have widths (that is, diameter, fora round spot) in the range from a minimum of about 10 μm to a maximum ofabout 1.0 cm. In embodiments where very small spot sizes or featuresizes are desired, material can be deposited according to the inventionin small spots whose width is in the range about 1.0 μm to 1.0 mm,usually about 5.0 μm to 500 μm, and more usually about 10 μm to 200 μm.Spot sizes can be adjusted as desired, by using one or a desired numberof pulses from a pulse jet to provide the desired final spot size.

[0031] The apparatus further includes a sensor in the form of a firstcamera 300 located to view fiducial markings on head 210 and/or thepositions of the nozzles on head 210. Typical fiducial markings areshown as fiducial markings 211 on the side of head 210 for visibility,although in practice fiducial marks viewed by first camera 300 may be onthe underside of head 210. A second sensor in the form of a secondcamera 304, is located to observe the positions of fiducial markings 18on substrate. Cameras 300 and 304 communicate with processor 140, andeach should have a resolution that provides a pixel size of about 1 to100 micrometers and more typically about 4 to 20 micrometers or even 1to 5 micrometers. Any suitable analog or digital image capture device(including a line by line scanner) can be used for such camera, althoughif an analog camera is used processor 140 should include a suitableanalog/digital converter. Further, other numbers of cameras may be used.For example, a single camera with the correct orientation andparameters, could be used in place of cameras 300 and 304. A display310, speaker 314, and operator input device 312, are further provided.Operator input device 312 may, for example, be a keyboard, mouse, or thelike. Processor 140 has access to a memory 141, and controls print head210 (specifically, the activation of the ejectors therein), operation ofthe positioning system, operation of each jet in print head 210, captureof images from the cameras, and operation display 310 and speaker 314.Memory 141 may be any suitable device in which processor 140 can storeand retrieve data, such as magnetic, optical, or solid state storagedevices (including magnetic or optical disks or tape or RAM, or anyother suitable device, either fixed or portable). Processor 140 mayinclude a general purpose digital microprocessor suitably programmedfrom a computer readable medium carrying necessary program code, toexecute all of the fucntions required of it as described below. It willbe appreciated though, that when a “processor” such as processor 140 isreferenced throughout this application, that such includes any hardwareand/or software combination which will perform the required functions.For example, for errors in the transport system, a corrected drivepattern can be produced by programming a device such as the ProgrammableError Correction PKE 80, available form RSF Electronik, Rancho Cordova,Calif., USA, with measured error data obtained from examining thetransport system of the deposition apparatus apparatus. A microprocessorwhich provides the target drive pattern, together with the foregoingprogrammed device, then operates as a “processor” of the presentinvention. The programming can be provided remotely to processor 140, orpreviously saved in a computer program product such as memory 141 orsome other portable or fixed computer readable storage medium using anyof those devices mentioned below in connection with memory 141. Forexample, a magnetic or optical disk 324 may carry the programming, andcan be read by disk reader 326.

[0032] Operation of the apparatus of FIG. 4 in accordance with a methodof the present invention, will now be described with reference to thatFIG. and FIG. 5. First, it will be assumed that memory 141 holds atarget drive pattern. This target drive pattern is the instructions fordriving the apparatus components as required to form the target array(which includes target locations and dimension for each spot) onsubstrate 10 and includes, for example, movement commands totransporters 60 and 100 as well as firing commands for each of the pulsejets in head 210 coordinated with the movement of head 210 and substrate10, as well as instructions for which polynucleotide solution (orprecursor) is to be loaded in each pulse jet (that is, the “loadingpattern”). This target drive pattern is based upon the target arraypattern and can have either been input from an appropriate source (suchas input device 312, a portable magnetic or optical medium, or from aremote server, any of which communicate with processor 140), or may havebeen determined (402) by processor 140 based upon an input target arraypattern (using any of the appropriate sources previously mentioned) andthe previously known nominal operating parameters of the apparatus(400). Further, it will be assumed that drops of different biomonomer orbiopolymer containing fluids (or other fluids) have been placed atrespective regions of a loading station (not shown). Operation of thefollowing sequences are controlled by processor 140, following initialoperator activation, unless a contrary indication appears.

[0033] For any given substrate 10, the operation is basically follows:(i) determine (402) target drive pattern (if not already provided) toobtain target array pattern, based on nominal operating parameters andtarget polynucleotide array pattern; (ii) examine (406) operatingparameter data (404) from sensors 300, 304 for an error from a nominalvalue, which error will result in use of the target drive patternproducing a discrepancy between the target array pattern and an actualarray pattern which would be deposited if the target drive pattern wasused; (iii) if there is no error in one or more operating parameters(406) then the apparatus is operated according to the target drivepattern; (iv) if there is an error in one or more operating parameters(406) then processor 140 derives, based on the error, a corrected drivepattern from the target pattern such that use of the corrected drivepattern results in a reduced discrepancy between the target and actualarray patterns than would have occurred if the target drive pattern hadbeen used.

[0034] It will be appreciated that any discrepancy between a nominalparameter and an actual sensed parameter, may optionally only beclassified as an “error” in an operating parameter, if it meets orexceeds a predetermined threshold value. Particular examples ofoperating parameter errors which may occur in the apparatus of FIG. 4include any one or more of the following:

[0035] 1. Substrate 10 may be incorrectly positioned with respect toencoder 30 or encoder 34.

[0036] 2. Head 210 may be incorrectly positioned with respect to encoder34 or, where there are multiple heads 210 in the apparatus, one or moreof them may be incorrectly positioned with respect to each other.

[0037] 3. Head 210 may be skewed (orientation error), and thus itsnozzles vary from their desired positions and/or orientations withrespect to encoder 34.

[0038] 4. Either encoder 30, 34 may have intrinsic errors, due to whichit will report an incorrect position.

[0039] 5. Either substrate 10 or either encoder 30, 34 may suffer fromthermal expansion.

[0040] 6. The transporter 60 and carriage 62 used to move the substratein the direction of nominal axis 63 (orthogonal to the direction 204ofscanning of head 210) may also have intrinsic errors, suffer fromthermal expansion, or operate at a deviation to nominal axis 63 (anon-straight deviation in the direction of axis 204 and/or a non-flatdeviation in the direction of axis 202). In addition, componentimperfections may cause the transport to suffer from Abbe errors.

[0041] 7. The nozzles of head 210 may fire at an angle to that intended.The above operating parameter errors can be sensed and used by processor140 to derive an actual drive map as follows:

[0042] 1. The actual position of substrate 10 can be determined byobservation of fiducial marks 18 by camera 304. If different substratesare repeatedly placed on substrate station 20, this error can bedetermined each time it is placed.

[0043] 2. The position of head 210 can be determined by observation offiducial marks 211 and/or the nozzles themselves by camera 300. In apreferred embodiment, the same camera is used for this observation andobservation of substrate fiducials 18, this scheme having the advantagethat no inter-camera calibration is required.

[0044] 3. Same as in 2.

[0045] 4. Laser-interferometer mapping of the errors in the encoders isa method well established in the art, and will provide a measurement ofthe relative error at many points along the encoder.

[0046] 5. Thermal expansion can be measured by repeated observation ofsubstrate fiducial marks 18 by camera 304, and by repeated observationof head fiducial marks 211 after movement by camera 300 or optionally bytwo cameras. Alternatively, a thermistor could be used and an expectedthermal expansion calculated.

[0047] 6. Errors in operation of transporter 60 and carriage 62 can bemapped by means of camera 304, and thermal expansion mapped byobservation of fiducial marks on carriage 62 by a camera (or optionallytwo cameras). Non-straightness and or flatness can be determined bylaser interferometry. Laser interferometry mapping of Abbe errors in atransport system generally, is a known technique.

[0048] 7. Test-print patterns can be observed with a camera (such ascamera 304) to observe drop placement. Suitable observations techniquesare described, for example, in co-pending U.S. patent application Ser.No. 09/302,898 filed Apr. 30, 1999 by Caren et al., assigned to the sameassignee as the present application, incorporated herein by reference.

[0049] The apparatus is then operated (410) as follows: (a) load head210 with a first set of polynucleotide containing solutions or theirprecursors (for example, a given head may be able to hold n differentmembers); (b) dispense droplets from head 210 onto substrate 10 or a setof substrates in accordance with the target or corrected drive patternsto provide the target array pattern for the first set on each ofmultiple arrays 12; and (c) repeat the foregoing sequence starting atstep (i) with a second set and subsequent sets of polynucleotidecontaining solutions or their precursors, until all required solutionshave been dispensed onto substrate 10 (for example, if each array hasm·n members, and presynthesized polynucleotides are being dispensed,then the sequence will be repeated m times). Optionally, as anothermeans of providing operating parameter data, the deposited arrays can beinspected by capturing one or more images such as from camera 304 andcomparing the deposited array pattern with the target array pattern.Differences in the foregoing may indicate particular types of errors(for example, a single nozzle of head 210 is oriented incorrectly withrespect to other nozzles of head 210). For example, an inspection couldbe performed on after step (b) in each cycle. Preferably, all arrays ona given substrate 10 have been inspected before shipping to an end user.The foregoing steps are discussed in more detail below.

[0050] The manner of correction provided by processor 140 can be morereadily understood by reference to FIGS. 6 through 8. In particular,FIG. 6 represents an image in memory 141 of a portion of the targetdrive pattern. It will be assumed that this pattern is created by adispensing head with a three by two matrix of dispensing jets (orientedwith three jets in the vertical direction of FIGS. 6-8 and two in thehorizontal direction), thus requiring a firing of all jets, followed byhead displacement and another firing of all jets. Hence FIG. 6corresponds to the appearance of the target array pattern if allrelevant components of the deposition apparatus are operating accordingto their normal parameters (“operating” in this context includes correctpositioning, whether static or dynamic). However, from observations ofprevious test prints by camera 300, processor 140 determines there is anerror in relative orientation of the nozzle of head 210 which producesspots 16 a. Similarly, an error is determined in fluid volumes depositedby the nozzle of head 210 which produces spots 16 b. Processor 140 thenderives a corrected drive pattern, the image in memory of the correcteddrive pattern being illustrated in FIG. 6. This corrected drive patternincorporates an inverse of the determined errors. That is, in order tocorrect for displacement (in the upward direction as viewed in FIG. 7)of spots 16 a, the actual drive image will contain an instruction tomove the head lower (as viewed in FIG. 8) than the nominal position ofFIG. 6 to compensate for the displacement in FIG. 7. Similarly, tocorrect for the below expected volume (that is, the nominal volume)produced by the jets producing features 16 b, the actual drive imagewill contain an instruction for that jet to fire multiple spots or withmore energy (this appearing as enlarged features 16 b in FIG. 8) tocompensate for the low volume error. Alternatively, the actual driveimage can be an instruction to switch to a different jet in the headwhen a deviation from nominal volume is encountered which may be morethan a predetermined tolerance, and to compensate for the differentposition of the different jet accordingly. While the illustrated errorsin FIG. 7 relate to individual spots, other errors can be general inthat they relate to all spots. For example, an error in the position ofsubstrate 10 on substrate station 20 is a general error, and thecorrected drive pattern could be the same as the target drive patternbut with the addition of a set of offset instructions to the positioningsystem, such as a single instruction to one or any combination oftransporters 60, 100, 120, to offset the position system from nominal tocompensate for this error.

[0051] A loading sequence for head 210 is more completely described inco-pending patent applications “FABRICATING BIOPOLYMER ARRAYS”, by Carenet al., Ser. No. 09/302,922, and “PREPARATION OF BIOPOLYMER ARRAYS” byA. Schleifer et al., Ser. No. 09/302,899, both filed Apr. 30, 1999 andboth assigned to the same assignee as the present application, and thereferences cited therein, including the possibility of using a flexiblemicrotitre plate as described in U.S. patent application “Method andApparatus for Liquid Transfer”, Ser. No. 09/183,604. Those referencesand all other references cited in the present application, areincorporated into this application by reference. Processor 140 cancontrol pressure within head 210 to load each polynucleotide solutioninto the chambers in the head by drawing it through the orifices.

[0052] Substrate 10 is loaded onto substrate station 20 either manuallyby an operator, or optionally by a suitable automated driver (not shown)controlled, for example, by processor 140.

[0053] The deposition sequence is then initiated to deposit the desiredarrays of polynucleotide containing fluid droplets on the substrate toprovide dried drops on the substrate according to the target patterneach with respective feature locations and dimensions. As alreadymentioned, in this sequence processor 140 will operate the apparatusaccording to the target or corrected drive pattern, by causing thepositioning system to position head 210 facing substrate station 20, andparticularly the mounted substrate 10, and with head 210 at anappropriate distance from substrate 10. Processor 140 then causes thepositioning system to scan head 210 across substrate 10 line by line (orin some other desired pattern), while co-ordinating activation of theejectors in head 210 so as to dispense droplets in accordance with thetarget pattern. If necessary or desired, processor 140 can repeat theload and dispensing sequences one or more times until head 210 hasdispensed droplets in accordance with the target or corrected drivepattern for all arrays 12 to be formed on substrate 10. The number ofspots in any one array 12 can, for example, be at least ten, at leastone hundred, at least one thousand, or even at least one hundredthousand.

[0054] At this point the droplet dispensing sequence is complete.

[0055] In an alternative to the above described embodiment the correcteddrive pattern, instead of being derived prior to beginning deposition ofdroplets, may be created “on the fly”. In one way of accomplishing this,the corrected drive pattern is created by modifying, based on thedetected error, instructions to at least one deposition apparatuscomponent which were based on the target drive pattern. This is doneduring the deposition of the probes or probe precursors. For example,the encoders 34 may be of a type which simply sends a pulse to the headat a certain spatial frequency; on each such pulse, the image fileinstructs the drive electronics which nozzles should be fired. Insteadof deriving a corrected drive pattern in memory 141 so that the encoderpulses will cause accurate printing, the encoder signals may beprocessed by processor 140 to cause a non-distorted image to printaccurately.

[0056] It is preferable in an apparatus, method, or computer program ofthe present invention, to not actually derive a target drive patternfrom a target array pattern, but instead to simply derive a correcteddrive pattern from the target pattern, nominal conditions and detectederror, when an error is detected. This can be done before fabrication ofa given array has started at least when the error is detected beforesuch fabrication has started (for example, as a result of examining anoperating parameter by examining a previously fabricated array), orduring such fabrication. Again, the target drive pattern may be saved inmemory or just derived during the actual array fabrication and sent asinstructions directly to the apparatus components.

[0057] The present methods and apparatus may be used to depositbiopolymers or other moieties on surfaces of any of a variety ofdifferent substrates, including both flexible and rigid substrates.Preferred materials provide physical support for the deposited materialand endure the conditions of the deposition process and of anysubsequent treatment or handling or processing that may be encounteredin the use of the particular array. The array substrate may take any ofa variety of configurations ranging from simple to complex. Thus, thesubstrate could have generally planar form, as for example a slide orplate configuration, such as a rectangular or square or disc. In manyembodiments, the substrate will be shaped generally as a rectangularsolid, having a length in the range about 4 mm to 1 m, usually about 4mm to 600 mm, more usually about 4 mm to 400 mm; a width in the rangeabout 4 mm to 1 m, usually about 4 mm to 500 mm and more usually about 4mm to 400 mm; and a thickness in the range about 0.01 mm to 5.0 mm,usually from about 0.1 mm to 2 mm and more usually from about 0.2 to 1mm. However, larger substrates can be used, particularly when such arecut after fabrication into smaller size substrates carrying a smallertotal number of arrays 12.

[0058] In the present invention, any of a variety of geometries ofarrays on a substrate 10 may be fabricated other than the organized rowsand columns of arrays 12 of FIG. 1. For example, arrays 12 can bearranged in a series of curvilinear rows across the substrate surface(for example, a series of concentric circles or semi-circles of spots),and the like. Similarly, the pattern of regions 16 may be varied fromthe organized rows and columns of spots in FIG. 2 to include, forexample, a series of curvilinear rows across the substrate surface(forexample, a series of concentric circles or semi-circles of spots), andthe like. Even irregular arrangements of the arrays or the regionswithin them can be used, at least when some means is provided such thatduring their use the locations of regions of particular characteristicscan be determined (for example, a map of the regions is provided to theend user with the array). The configuration of the arrays and theirfeatures may be selected according to manufacturing, handling, and useconsiderations.

[0059] The substrates may be fabricated from any of a variety ofmaterials. In certain embodiments, such as for example where productionof binding pair arrays for use in research and related applications isdesired, the materials from which the substrate may be fabricated shouldideally exhibit a low level of non-specific binding during hybridizationevents. In many situations, it will also be preferable to employ amaterial that is transparent to visible and/or UV light. For flexiblesubstrates, materials of interest include: nylon, both modified andunmodified, nitrocellulose, polypropylene, and the like, where a nylonmembrane, as well as derivatives thereof, may be particularly useful inthis embodiment. For rigid substrates, specific materials of interestinclude: glass; plastics (for example, polytetrafluoroethylene,polypropylene, polystyrene, polycarbonate, and blends thereof, and thelike); metals (for example, gold, platinum, and the like).

[0060] The substrate surface onto which the polynucleotide compositionsor other moieties is deposited may be smooth or substantially planar, orhave irregularities, such as depressions or elevations. The surface maybe modified with one or more different layers of compounds that serve tomodify the properties of the surface in a desirable manner. Suchmodification layers, when present, will generally range in thicknessfrom a monomolecular thickness to about 1 mm, usually from amonomolecular thickness to about 0.1 mm and more usually from amonomolecular thickness to about 0.001 mm. Modification layers ofinterest include: inorganic and organic layers such as metals, metaloxides, polymers, small organic molecules and the like. Polymeric layersof interest include layers of: peptides, proteins, polynucleic acids ormimetics thereof (for example, peptide nucleic acids and the like);polysaccharides, phospholipids, polyurethanes, polyesters,polycarbonates, polyureas, polyamides, polyethyleneamines, polyarylenesulfides, polysiloxanes, polyimides, polyacetates, and the like, wherethe polymers may be hetero- or homopolymeric, and may or may not haveseparate functional moieties attached thereto (for example, conjugated),Various modifications to the embodiments of the particular embodimentsdescribed above are, of course, possible. Accordingly, the presentinvention is not limited to the particular embodiments described indetail above.

What is claimed is:
 1. A method of fabricating an addressable array ofbiopolymer probes on a substrate according to a target array patternusing a deposition apparatus which, when operated according to a targetdrive pattern based on nominal operating parameters of the apparatus,provides the probes on the substrate in the target array pattern, themethod comprising: (a) examining at least one operating parameter for anerror from a nominal value which error will result in use of the targetdrive pattern producing a discrepancy between the target array patternand an actual array pattern deposited; (b) when an error is detectedderiving, based on the error, a corrected drive pattern different fromthe target drive pattern such that use of the corrected drive patternresults in a reduced discrepancy between the target and actual arraypatterns.
 2. A method according to claim 1, additionally comprisingoperating the deposition apparatus according to the corrected drivepattern.
 3. A method according to claim 1 wherein the probes are DNA orRNA probes.
 4. A method according to claim 1 additionally comprisingsaving the target drive pattern in a memory of the deposition apparatus.5. A method according to claim 1 additionally comprising saving thetarget drive pattern in a memory of the deposition apparatus, andwherein the corrected drive pattern is saved in the memory.
 6. A methodaccording to claim 1 wherein the corrected drive pattern is derivedwithout obtaining a target drive pattern.
 7. A method according to claim4 wherein: the deposition apparatus includes a dispensing head todispense fluid droplets containing the probes or probe precursors, and atransport system to move at least one of the dispensing head andsubstrate relative to the other as the droplets are dispensed from thehead, so as to form the array; and the drive pattern controls operationof the transport system.
 8. A method according to claim 1 wherein: thedeposition apparatus includes a dispensing head to dispense fluiddroplets containing the probes or probe precursors, and a transportsystem to move at least one of the dispensing head and substraterelative to the other as the droplets are dispensed from the head, so asto form the array; the drive pattern controls operation of the transportsystem; and the operating parameter is the position of the substrate ordispensing head, which is examined by viewing the substrate ordispensing head.
 9. A method according to claim 8 wherein the operatingparameter is examined by viewing a fiducial mark on the dispensing heador substrate
 10. A method according to claim 1 wherein: the depositionapparatus includes a dispensing head with multiple nozzles to dispensefluid droplets containing the probes or probe precursors, and atransport system to move at least one of the dispensing head andsubstrate relative to the other as the droplets are dispensed from thehead, so as to form the array; the drive pattern controls operation ofthe transport system; the operating parameter is the position of thesubstrate or dispensing head, or orientation of a nozzle, and isexamined by viewing the substrate, dispensing head, or nozzle, or adroplet pattern previously dispensed from the head.
 11. A methodaccording to claim 7 additionally comprising saving the target drivepattern in a memory of the deposition apparatus, and wherein thecorrected drive pattern is saved in the memory, prior to operating thedispensing head and transport system to form the array.
 12. A methodaccording to claim 7 additionally comprising saving the target drivepattern in a memory of the deposition apparatus, and wherein thecorrected drive pattern is derived by modifying, based on the detectederror, instructions to at least one deposition apparatus component basedon the target drive pattern during operation of the dispensing head andtransport system to form the array.
 13. A method according to claim 1wherein the at least one parameter is the position of the substrate inthe deposition apparatus.
 14. A method according to claim 7 wherein theat least one parameter is a position of the dispensing head.
 15. Amethod according to claim 7 wherein the deposition apparatus furtherincludes a position encoder to detect the position of the dispensinghead or the substrate, and wherein the at least one parameter is theaccuracy of the encoder.
 16. A method according to claim 7 wherein theat least one parameter is the accuracy in an ability of the transportsystem to move the substrate to an expected location in response to acommand.
 17. A method according to claim 7 wherein the dispensing headhas multiple droplet dispensing nozzles, and wherein the at least oneparameter is a position of a nozzle.
 18. A method of fabricating anaddressable array of biopolymer probes on a substrate according to atarget array pattern using a deposition apparatus which, when operatedaccording to a target drive pattern based on nominal operatingparameters of the apparatus and which is stored in a memory of thedeposition apparatus, provides the probes on the substrate in the targetarray pattern, the method comprising: when an error from a nominal valueexists in at least one operating parameter, which error will result inuse of the target drive pattern producing a discrepancy between thetarget array pattern and an actual array pattern deposited thenderiving, based on the error, a corrected drive pattern from the targetdrive pattern such that use of the corrected drive pattern results in areduced discrepancy between the target and actual array patterns.
 19. Amethod according to claim 18 wherein the corrected drive pattern issaved in the memory.
 20. A method of fabricating an addressable array ofbiopolymer probes on a substrate carrying at least one fiducial mark,using a fabrication apparatus which includes a dispensing head todispense fluid droplets containing the probes or probe precursors, themethod comprising observing the at least one fiducial mark and, basedupon the observation, rotating the substrate to a predetermined angularrelationship with respect to the dispensing head.
 21. An apparatus forfabricating an addressable array of biopolymer probes on a substrateaccording to a target array pattern which apparatus, when operatedaccording to a target drive pattern based on nominal operatingparameters of the apparatus, provides the probes on the substrate in thetarget array pattern, the apparatus comprising: (a) a sensor whichsenses at least one operating parameter for an error from a nominalvalue which error will result in use of the target drive patternproducing a discrepancy between the target array pattern and an actualarray pattern deposited; (b) a processor which, when an error isdetected by the sensor derives, based on the error, a corrected drivepattern different from the target drive pattern such that use of thecorrected drive pattern results in a reduced discrepancy between thetarget and actual array patterns.
 22. An apparatus according to claim 21additionally comprising: a dispensing head to dispense fluid dropletscontaining the probes or probe precursors, and a transport system tomove at least one of the dispensing head and substrate relative to theother as the droplets are dispensed from the head, so as to form thearray; and wherein: the drive pattern controls operation of thetransport system; the operating parameter is the position of thesubstrate or dispensing head; and the sensor views the substrate ordispensing head to obtain its position.
 23. An apparatus according toclaim 22 wherein the sensor views a fiducial mark on the dispensing heador substrate
 24. An apparatus according to claim 21 additionallycomprising: a dispensing head with multiple nozzles to dispense fluiddroplets containing the probes or probe precursors, and a transportsystem to move at least one of the dispensing head and substraterelative to the other as the droplets are dispensed from the head, so asto form the array; and wherein: the drive pattern controls operation ofthe transport system; the operating parameter is the position of thesubstrate or dispensing head, or orientation of a nozzle; and the sensorviews the substrate, dispensing head, or nozzle, or a droplet patternpreviously dispensed from the head.
 25. An apparatus according to claim21 additionally comprising a memory accessible by the processor to savethe target drive pattern, and wherein the processor, when no error isdetected, causes the apparatus to operate in accordance with the targetdrive pattern.
 26. An apparatus according to claim 21 comprising amemory accessible by the processor to save the target drive pattern, andwherein the processor: when no error is detected, causes the apparatusto operate in accordance with the target drive pattern; and when anerror is detected and a corrected drive pattern derived by theprocessor, saves the corrected drive pattern is saved in the memory. 27.An apparatus according to claim 21 wherein the processor derives thecorrected drive without obtaining a target drive pattern.
 28. Anapparatus according to claim 21 additionally comprising: a dispensinghead to dispense fluid droplets containing the probes or probeprecursors; and a transport system to move at least one of thedispensing head and substrate relative to the other as the droplets aredispensed from the head, so as to form the array; and wherein theprocessor controls operation of the transport system in accordance withone of the drive patterns.
 29. An apparatus according to claim 28wherein the processor saves the target drive pattern in the memory, andsaves the corrected drive pattern in the memory prior to operating thedispensing head and transport system to form the array.
 30. An apparatusaccording to claim 21 additionally comprising a memory accessible by theprocessor, wherein the processor saves the target drive pattern in amemory of the deposition apparatus; and the processor derives thecorrected drive pattern by modifying, based on the detected error,instructions to at least one apparatus component based on the targetdrive pattern during deposition of the probes to form the array.
 31. Anapparatus according to claim 25 wherein the at least one parameter isthe position of the substrate in the deposition apparatus.
 32. Anapparatus according to claim 28 wherein the at least one parameter is aposition of the dispensing head.
 33. An apparatus according to claim 28additionally comprising a position encoder to detect the position of thedispensing head or the substrate, and wherein the at least one parameteris the accuracy of the encoder.
 34. An apparatus according to claim 28wherein the at least one parameter is the accuracy in an ability of thetransport system to move the dispensing head or substrate to an expectedlocation in response to a command.
 35. An apparatus according to claim34 wherein the transporter moves the dispensing head or substrate alonga corresponding nominal axis, and wherein the at least one parameter isthe deviation of actual movement from the corresponding nominal axis.36. An apparatus according to claim 28 wherein the dispensing head hasmultiple droplet dispensing nozzles, and wherein the at least oneparameter is a position of a nozzle.
 37. An apparatus for fabricating anaddressable array of biopolymer probes on a substrate according to atarget array pattern, comprising (a) a memory to store a target drivepattern based on nominal operating parameters of the apparatus toprovide the probes on the substrate in the target array pattern; (b) aprocessor to receive an indication of an error from a nominal value inat least one operating parameter, which error will result in use of thetarget drive pattern producing a discrepancy between the target arraypattern and an actual array pattern deposited, and to derive a correcteddrive pattern from the target drive pattern such that use of thecorrected drive pattern results in a reduced discrepancy between thetarget and actual array patterns.
 38. An apparatus for fabricating anaddressable array of biopolymer probes on a substrate carrying at leastone fiducial mark, the apparatus comprising: a dispensing head todispense fluid droplets containing the probes or probe precursors; asensor to sense the position of the at least one fiducial mark on thesubstrate, and a transporter which based on the position of the at leastone fiducial marked as sensed by the sensor, can rotate the substrate toa predetermined angular relationship with respect to the dispensinghead.
 39. An apparatus according to claim 37 wherein the corrected drivepattern is saved in the memory.
 40. A computer program product, for useon an apparatus for fabricating an addressable array of biopolymerprobes on a substrate according to a target array pattern whichapparatus, when operated according to a target drive pattern based onnominal operating parameters of the apparatus, provides the probes onthe substrate in the target array pattern; the program productcomprising: a computer readable storage medium having a computer programstored thereon which, when loaded into a computer of the apparatusperforms the steps of: (a) receiving a signal from a sensor which sensesat least one operating parameter for an error from a nominal value whicherror will result in use of the target drive pattern producing adiscrepancy between the target array pattern and an actual array patterndeposited; and (b) when an error is detected by the sensor, deriving,based on the error, a corrected drive pattern different from the targetdrive pattern such that use of the corrected drive pattern results in areduced discrepancy between the target and actual array patterns.
 41. Acomputer program product according to claim 40, wherein the programadditionally performs the step of operating the apparatus according tothe corrected drive pattern.
 42. A computer program product according toclaim 41, wherein the program additionally performs the steps of savingthe target drive pattern in a memory of the apparatus, and saving thecorrected drive pattern in the memory prior to operating the apparatusaccording to the corrected drive pattern.
 43. A computer program productaccording to claim 41 wherein the program additionally performs thesteps of: saving the target drive pattern in a memory of the depositionapparatus; and deriving the corrected drive pattern by modifying, basedon the detected error, instructions to at least one apparatus componentbased on the target drive pattern, during deposition of the probes toform the array.
 44. A computer program product, for use on an apparatusfor fabricating an addressable array of biopolymer probes on a substrateaccording to a target array pattern which apparatus, when operatedaccording to a target drive pattern based on nominal operatingparameters of the apparatus, provides the probes on the substrate in thetarget array pattern the program product comprising: a computer readablestorage medium having a computer program stored thereon which, whenloaded into a computer of the apparatus performs the steps of: (a)storing the target drive pattern in a memory; (b) receiving an inputsignal indicating an error from a nominal value in at least oneoperating parameter, which error will result in use of the target drivepattern producing a discrepancy between the target array pattern and anactual array pattern deposited; and (c) deriving a corrected drivepattern from the target drive pattern such that use of the correcteddrive pattern results in a reduced discrepancy between the target andactual array patterns.
 45. A computer program product according to claim44, wherein the program additionally performs the step of operating theapparatus according to the corrected drive pattern.